MT1-MMP-TIMP-1 complex

Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1)


The human matrix metalloproteinases (MMPs) family comprises a large group of structurally homologous zinc-dependent endopeptidases (e.g. membrane type-1 matrix metalloproteinase (MT1-MMP) (darkmagenta) and membrane type-3 matrix metalloproteinase (MT3-MMP) (magenta), click to see structural comparison ) that perform a wide variety of biological roles. In general, the MMPs are inhibited unselectively by all four known tissue inhibitors of metalloproteinases (TIMPs 1-4) which have 40-50% sequence identity. For example, membrane type-3 matrix metalloproteinase (MT3-MMP) can form complex with wild-type TIMP-1 (1uea, colored orange ). The WT-TIMP-1 binding interface (cyan) is mainly composed of the N-terminal segment that approaches the active site, the AB loop (Thr33-Tyr35), the CD loop (Ala65-Cys70), and the EF loop (Thr97-Ser100). The pivotal residue, threonine 98 (Thr98), is shown as red sticks. In general, five main chain hydrogen bonds (Cys1-Ser68, Val69-Met66, Gly71-Met66, Cys70-Glu67, and Cys70-Thr98) are intimately involved in the conformational stability of TIMP binding interface when bound to MMP. Membrane type-1 matrix metalloproteinase (MT1-MMP) (darkmagenta) also forms complex with wild-type TIMP-1 (2j0t, <font color='orange'>colored orange ), producing <scene name='MT1-MMP-TIMP-1_complex/Cv2/12'>similar hydrogen bond network in the WT TIMP-1 binding interface as well as <scene name='MT1-MMP-TIMP-1_complex/Cv2/13'>in the case with MT3-MMP. This network of hydrogen bonds stabilizes the CD and EF loops that compose the binding interface. Importantly, the <scene name='MT1-MMP-TIMP-1_complex/Cv2/14'>hydrogen bond between Cys1 and Ser68 may position the amino and carboxyl groups of Cys1 to effectively coordinate the Zn2+ ion. However, this MT1-MMP-WT-TIMP-1 complex is not tight-binding. MT1-MMP is unique since even though it exhibits high structural homology to all MMPs, it is not inhibited by TIMP-1, <scene name='MT1-MMP-TIMP-1_complex/Cv3/1'>but is inhibited by the structural homologous TIMP-2 (1bqq). <scene name='MT1-MMP-TIMP-1_complex/Cv2/15'>The single point mutation T98L (mutant TIMP-1 is colored in yellow with <font color='red'>T98L shown in red ) transformed TIMP-1 into a high affinity inhibitor of MT1-MMP (3ma2). WT-TIMP-1, WT-TIMP-2, and TIMP-1 T98L mutant have kinetic dissociation binding constant (KD) 1.53 x 10-6, 5.61 x 10-8, and 8.70 x 10-8, respectively. So, KD of WT-TIMP-2 is 2 orders of magnitude smaller than that of WT-TIMP-1, indicating the weak affinity between MT1-MMP and WT-TIMP-1. The TIMP-1 T98L mutant regained high-affinity binding to MT1-MMP, resulting in a 2 order of magnitude decrease in KD, similar to the case for WT-TIMP-2, the in vivo inhibitor of MT1-MMP. The overall structures of the complexes of <font color='darkmagenta'>MT1-MMP -<font color='orange'>WT-TIMP-1 and <font color='violet'>MT1-MMP - mutant-T98L-TIMP-1 are <scene name='MT1-MMP-TIMP-1_complex/Cv2/17'>relatively similar. Even the structure of <font color='magenta'>MT3-MMP -<font color='orange'>WT-TIMP-1 is <scene name='MT1-MMP-TIMP-1_complex/Cv2/18'>similar to those of MT1-MMP-TIMP-1s (with <font color='orange'>wild-type and TIMP-1 T98L mutant ). <scene name='MT1-MMP-TIMP-1_complex/Cv4/1'>Leu98 is pointing toward MT1-MMP residues Pro259 and Phe260, establishing a strong hydrophobic core, which is situated near the MT1-MMP <scene name='MT1-MMP-TIMP-1_complex/Cv4/3'>catalytic Zn2+ ion surrounded by His239, His243, and His249. So, this T98L replacement may stabilize the entire area by establishing a strong hydrophobic core upon binding to the enzyme. However, it seems unlikely that these additional bonds could account for the entire binding effect between MT1-MMP and TIMP-1. Statistical analysis of the <scene name='MT1-MMP-TIMP-1_complex/Cv2/15'>key hydrogen bond stabilities in the TIMP-1 T98L mutant reveals that the hydrogen bonds network in mutant form is significantly more stable than that in WT-TIMP-1. Mutations that enhance hydrogen bond stability contribute to the stability of the bound-like, less flexible, conformation of TIMP-1, which eventually results in increasing binding affinity for MT1-MMP. Thus, mutation affected the instrinsic dynamics of the inhibitor rather than its structure, thereby facilitating the interaction.

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3D structures of MMP
Matrix metalloproteinase